For years, the Cook County Circuit Clerk’s office has argued that the city of Chicago owes the court millions of dollars in unpaid fees.That disputed tab sits at $13.2 million, according to Jalyne R. Strong-Shaw, a spokeswoman for Circuit Clerk Dorothy A. Brown.Now, state lawmakers have weighed in, siding with the city.In the waning hours of its spring session, the General Assembly passed legislation stating municipalities and school districts do not have to pay a fee to file ordinance-enforcement actions, civil debt …